Parallels
by Observer Gemini
Summary: After a mysterious malfunction of the TARDIS, the Doctor and the Ponds crash land in a parallel universe. Only problem is the Doctor is in a coma and the Ponds are treated like common criminals and are soon experimented upon by a mad scientist...


**Prologue: The Arrival **

**Charles River**

**Outside Harvard University**

It was an average sunny spring afternoon at Harvard University as its students and staff were getting ready to finish the semester. The sun was high in the sky, unimpeded by any wifts of clouds and several students were out on the river relaxing in between intense study sessions.

Suddenly the blissful silence was broken by the most remarkable sound - that of ancient engines grinding. Most intriguing of all was that this sound was coming from high up in the air and there was a bright light in the sky as the outline of a little blue box appeared out of nowhere. All the people on the Charles River and the campus of Harvard University stopped in their tracks with startled and gaping expressions. As the outline of the little blue box became clearer, an older gentleman and a trio of young people burst out of one the University's buildings to take in this strange sight for themselves.

"What is it, Walter?" the young woman with frizzy black hair asked from beside the elderly gentleman with wild grey hair and dressed in a cardigan sweater.

"Hush, Astro!" he said distractedly as he stared open mouthed as the little blue box finally materialized high in the sky above the Charles River and began to descend wildly to the middle of the river.

"It appears to be out of control, whatever it is..." the young man said, draping an arm over the slender blonde woman at his side.

"What is it? A ship?" The blonde woman asked, not tearing her eyes from it as it spun wildly out of control and its doors opened and a trio of figures shot out of it at a terrific speed.

"Whoa...!" the young woman with frizzy hair gasped as the figures fell into the water shortly before their box crashed in a short distance away from them.

"Come on, Peter, we have to see if they're ok! Astrid, call for a Science Division medical team!" the blonde woman ordered frantically as she and the young man dashed for the river.

Astrid nodded as she touched her earbud on her right ear. "This is Agent Farnsworth requesting a medical team to the Charles River. Yes, Three unidentified persons fell out of the UFO into the river. Fringe Agents are on the scene now. Thanks." she said before trotting after the agents she just mentioned with Walter, the elderly gentleman, shuffling behind her.

Unbeknownst to them and all the other onlookers at the scene, a tall man in a dark suit wearing a fedora raised a phone to his ear without a word at a nearby park bench. "Yes, they have arrived." the man spoke flatly into the strange phone before closing it.

Peter and the young blonde woman were wading into the shallows of the Charles River when Astrid and Walter caught up with them while some students in a pair of canoes were rapidly paddling towards them with the unconscious bodies of the UFO's crew.

"Are they...?" Astrid asked from the shore as the canoes approached the shallows were Peter and the other Fringe agent were waiting.

"They're alive, just unconscious from the fall." Peter said, not tearing his eyes from the canoes.

"The Medical Teams are on their way." Astrid nodded in relief as Peter and the young blonde agent helped the student lay the unconscious trio on the sandy shore of the river.

"They're not even properly attired for spaceflight, at all! It's no wonder their ship malfunctioned! Just look at what this man is wearing!" Walter laughed as the four of them examined the unconscious crew.

There was a strangely dressed young man with wild dark hair in between a young woman with fiery hair and a young man who bore resemblance to Peter. The man in the middle was wearing tweed and a bowtie, the redheaded woman was dressed in a skirt, and the young man wore a flannel shirt under a vest with dark jeans.

"Injuries?" Walter asked as Peter and the other agent bent down to examine the trio.

"No physical ones that I can find. They'll need a proper examination in the medical wing of the new Science Division though..." the blonde agent replied as sirens could be heard in the distance as the medical teams began to arrive.

"Right on time." Peter nodded as various men and women in black Fringe Division uniforms began to pile out of the ambulances followed by the white uniformed men and women of the medical division bearing three stretchers.

"Make a path, folks! Make a path! Fringe Division!" the agents ordered gruffly as they pushed their way through the growing crowd of onlookers at the scene.

"Agents." the blonde agent nodded as the Fringe Agents approached with the stretchers.

"Agent Dunham." the lead agent nodded in response as the medics carefully laid the bodies on the stretchers and prepared to move them to the ambulances.

"Are there any other casualties?"

"None that we are aware of. But we will be needing transport for the UFO that crashed into the river. Dr. Bishop will undoubtedly want to examine it for himself before Science Division gets their hands on it." Dunham said briskly as the medics soon had the unconscious bodies secured in the ambulances and rushed to the Medical Facility at the Science Division.

"Yes, Ma'am. Our Agents will have it secured and brought to Dr. Bishop's lab within the hour."

"Alright, if that's everything, Agent Bishop and I will be at the Medical Facility overseeing the status of our visitors."

The Fringe Agent nodded as he and his men got to work retrieving the mysterious blue box from the river with Walter supervising from the sidelines.

"Be careful, you fools! You're damage it even more! What sort of Fringe Agents are you, AMATEURS?" he complained gruffly as Astrid sighed and closed her eyes before nodding at Agent Dunham. She and Walter had everything under control.

**Christmas Day, 2011**

**The Pond Residence**

Mr and Mrs. Pond were just sitting down to Christmas Dinner when there came a soft knock on the door. They looked at each other briefly before Mrs. Pond got up looking very annoyed at this latest interruption.

"Were you expecting company, Rory? I didn't invite anybody..."

"Nope." Rory said from his seat as Mrs. Pond made her way to the door.

As she made her way to the door, Mrs. Pond grabbed a water pistol from a nearby table. "If that is more carol singers, I have a water pistol! You're not gonna want to be all wet on a night like this!" she said as she opened the door with the aforementioned pistol raised.

She stopped in her tracks in shock when she saw who the unexpected visitor was - The Doctor.

"Not absolutely sure..." he began uncertainly, "how long?"

"Two years." Mrs. Pond said in a clipped voice as she squirted him a few times with her water pistol.

The Doctor took the shots, not even flinching. The two stood there, looking at each other in silence for a moment before Mrs. Pond squirted him a few more times for good measure.

"Ok, fair point." he finally said, breaking the silence.

"So, you're not dead."

"And, a Happy New Year!" he said with that childlike grin Mrs. Pond adored so much.

"River told us." Mrs. Pond said coldly, not wanting to embrace him just yet. She wanted him to know how much she had been hurt by his absence.

"Well, of course she did." The Doctor sighed.

"She's a good girl." Mrs. Pond said, defending her daughter.

After another uncomfortable moment of silence, Mrs. Pond said, "Well, I'm not going to hug first."

"Nor am I." The Doctor said just as obstinately as he turned his head away from her. He didn't want to look at her knowing full well that he would give in if he continued to look into her eyes.

The two stood there in yet another awkward moment of silence as the Doctor looked around at anything but Mrs. Pond and she fiddled with the water pistol still in her hand. The two finally looked at one another and then tore their gazes away. They kept doing this little game for a few more tense moments before the Doctor finally locked gazes with Mrs. Pond and gave her one of his smiles and she gave up the act and laughed and smiled as well. Finally, the two embraced as the two old friends ought to have done as soon as the door was opened.

"Mr. Pond!" Mrs. Pond called over her shoulder as she stepped out of the embrace after a long moment. "Guess who's coming for dinner!"

Mr. Pond came down the main hall, wrapping his cardigan around himself as he confronted his old friend. "You're not dead then?"

Mrs. Pond laughed once more. "We've done that."

"Oh, ok." Mr. Pond said disappointedly.

"We're about to have Christmas Dinner. Joining us?" She asked, turning back to her old friend, the Doctor.

"If it's no - "

"Trouble?" Mrs. Pond finished for him with a smile.

"There's a place set for you." Mr. Pond offered.

The Doctor looked confused for a brief moment. "But you didn't know I was coming. Why would you set me a place?"

Mrs. Pond smiled once more. "Oh, because we always do."

After another brief moment of silence between the old friends, she continued. "It's Christmas, you moron!"

After Mr. and Mrs. Pond had left for the dining room where the mentioned Christmas Dinner was waiting, the Doctor stood alone on the doorstep in silence. He touched his cheek. It felt wet. He had shed a tear. Odd. He smiled and then laughed silently to himself. After all these years alone, he finally had a family again. He shut the door with a smile and went to join his new family for Christmas Dinner.

Just as the trio were about to all sit down, there came yet another knock on the door. Mr. and Mrs. Pond shared another annoyed look across the table.

"Carolers?" The Doctor guessed.

"You bet." Mrs. Pond said, grabbing her water pistol again before stomping to the front door, cocking her weapon.

"I thought I told you guys we didn't -" she broke off as she opened the door to find her daughter standing on the doorstep with a broad smile. She was dressed in an elegant red dress with matching high heels.

"Hello, Mommy Dearest. I'm not late, am I? I did so hope to have Christmas Dinner with you and Father. And, is that my Husband I smell?" she said as she pushed her way past Mrs. Pond and into the dining room.

"River?" The Doctor and Rory said in surprise as they stood up from their seats as she entered the room.

"Hello, Father. And, Hello, Sweetie!" River said, giving one of her sexy, flirty winks to the Doctor. The Doctor sighed with a smile as he walked towards her.

"River, I should have known you'd be showing up if I appeared..." he said as they embraced.

"I would have shown up regardless. It is Christmas after all. And, I'd be an awful daughter if I didn't visit my parents during the holidays."

"Right." The Doctor said as he led her to her seat where a place was already set. Clearly, the Ponds had been expecting both the Doctor and River to show up tonight.

After a feast of turkey with all the fixings and gift giving and much merriment afterwards, the party was nearing an end as was the night. The Doctor stood up from his seat next to River on the couch in the living room adjacent to the Ponds' dining room.

"Well, it's time for one last Christmas present for you all - one last jaunt in the TARDIS!" he smiled.

"Where or When are we going, Doctor?" Mrs. Pond inquired. She had so missed traveling in Time and Space with the Doctor.

"Any Star, Any Planet, Anywhere and Anywhen you ever wanted to go! Your choice, Mr. and Mrs. Pond and you too, River!" The Doctor laughed.

"I'm sorry, but this time I won't be able to join you guys. I already have another engagement for tonight." River apologized.

"Ah, a future version of me is taking you somewhere, is he?" the Doctor smiled knowingly.

"I guess it can't harm you since you already guessed as much. Yes, you are."

"Where?" The Doctor asked, knowing he was already pressing his luck.

"The Singing Towers of Darillium in fact." River smiled as the Doctor stepped back a bit and his face grew deeply sad.

"Doctor, what's wrong? What is it?" asked in concern as she laid a hand on his arm as he sank back down on the couch.

"Well, goodbye then, River. I'll see you in a bit." he said in a hoarse whisper, giving her a strained smile.

"Doctor, what aren't you telling me?" River said, narrowing her eyes.

"Oh, its nothing. I just got a bit light headed is all. Nothing to fret over, Sweetie." The Doctor smiled broadly as if nothing had happened. "Go, enjoy yourself with future me! Have fun!" he said back to his normal self.

River cocked her head, suspicion on her face. But it soon passed and she smiled as she embraced her parents and then the Doctor. "Merry Christmas everyone!" she said as she pressed a few buttons on her vortex manipulator on her wrist and vanished.

"Alright, Doctor. What was that?" Mrs. Pond demanded once River had gone.

"You heard her, Amelia. She's going with the future version of me to the Singing Towers of Darillium..." the Doctor choked on the last part.

"What's so bad about that? It sounds like a nice date for the two of you..." Mrs. Pond said slowly as the pieces of the puzzle slowly moved into place in her mind's eye.

"It's not what happens on the date but what happens after." The Doctor finally admitted after a long moment of contemplation. "She'll see me one final time after that date... Our last meeting."

"What happens to her, Doctor! Tell me, what happens to our daughter!" Mrs. Pond cried, kneeling on the floor next to him her hand clasped in his.

"You must promise not to tell her a word of this, not a word!" The Doctor said earnestly.

"What is it, Doctor." Mrs. Pond pressed.

"She sacrifices herself for me and countless others." The Doctor finally said in a hoarse whisper. "She dies."

"Thank you for telling us, Doctor." Mrs. Pond said, closing her eyes to compose herself.

"Don't fret, Amelia. This isn't the last time you will see her. You'll see the earlier versions of her when she visits. Trust me." he smiled.

"Ok." Mrs. Pond whispered.

"So, ready to go?" The Doctor smiled, trying to distract the Ponds from the recent revelation he had just dropped on them.

"Yes, let's just get this over with." Mrs. Pond said, trying to be pleasant in the face of her daughter's imminent death.

And, with that the Doctor and the Ponds were off for one last jaunt in the TARDIS for an unknown destination.

**Fringe Division Headquarters, Boston**

**Science Division - Medical Wing**

Amy woke with a start and didn't recognize her surroundings at all. She appeared to be in some sort of advanced medical facility. As she tried to get out of bed, she found her legs and arms handcuffed to the bed as well as several IVs stuck in her arm.

"Oi, what is the meaning of this! Why am I cuffed to this bed!" she hollered in outrage.

The only response she got was the continued silence of the room accompanied by the occasional beep of the medical machinery around her bed. She looked frantically around for her husband, Rory or any sign of the Doctor. But, she was alone in the room save for the machines monitoring her vital signs.

Just as she was about to give up hope, the door to the room clicked as it was unlocked from the outside and opened as a female medic in a white uniform walked in followed by a pair of guards in black uniform. Most unnerving was the fact that they had their weapons drawn and pointed at Amy.

"Uh, what is all this about and where am I?" Amy gulped as the guards closed the door and stationed themselves on either side of it as the medic approached Amy.

"I'm just here to check your vitals, hun." she smiled as she glanced at the machines briefly and shone a penlight into Amy's eyes.

"Your vitals are fine and you appear to be recuperating. A medic will be here shortly with some food and drink." she said before exiting the room with the guards once more before locking the door behind her.

Amy slumped back down into her pillow and closed her eyes with a sigh. Where in the Universe was she? What had happened? Why was she being treated like some common criminal? And, where were the Doctor and Rory?

She was awoken from her doze as the door opened yet again. _Oh, good, it must be the medic with the food and drink, I am feeling a bit hungry_, she thought. But, she was disappointed to see a young blonde woman enter with no food or drink in sight. What was odd was that no guards accompanied this woman.

"No guards? Aren't you brave!" Amy said lightly, although she felt the complete opposite.

"Rest assured, you are being monitored via security cameras and there are guards posted in every hall outside this room. No sooner would you have escaped from this room then you would be shot on sight." the woman smiled coldly.

"Is that so..." Amy gulped, fear gripping her. What had she done to deserve this?

"Now, I and my superiors would like to know who you are, where you are from, who you work for, and what your purpose here is."

"Excuse me?" Amy asked, baffled by all these questions.

"Do you or do you not work for William Bell. Answer the questions and you may see the light of the sun again. They are simple questions!"

Amy frowned at the young blonde woman. These questions were beyond simple in her mind.

"My name is Amy Pond. I'm from a planet called Earth in the 21st Century. I work for no one, I'm a housewife. I have no purpose here, I was with friends traveling." she said calmly.

"Enough of the lies. I want the truth. And, be aware Fringe Division has the authority and the technology to get you to talk." the woman said coldly, folding her arms.

Amy closed her eyes, she had the feeling this would be a very long day, indeed.

"I just did! Now, I want answers from you! For starters, where am I? What planet am I on? Where is my husband and my friend? What happened to us? And, furthermore, why am I being treated like a petty criminal?"

The woman remained silent and left the room looking furious, yet concerned. Amy sighed. She wondered how long she would be kept in this room. She shed a tear as she wondered where Rory was and what had happened to him and the Doctor. The last thing she remembered was the TARDIS malfunctioning before she, Rory, and the Doctor had been tossed out the doors on some unnamed planet and time.

"Well, did you get anything from her?" General Broyles demanded as soon as Olivia had locked the door and turned around. His arms were crossed across his torso.

"Nothing at all, sir. She appears to be suffering from some sort of delusions." Olivia said with a sigh as Peter stepped away from the wall he had been leaning against and took her hand.

"Delusions?" Peter asked.

"She is of the belief she is on a different planet and maybe in a different time from her own. She also claims to be traveling with her friends."

"You had better call Dr. Bishop then." Broyles said after a moment.

"Question them?" Peter inquired.

"Question them." Broyles nodded as he departed down the hall leaving Peter and Olivia alone.

"How are the other two doing?" Peter asked after a moment.

"Come with me. You'll have to see it to believe it." Olivia sighed as she led him down the hall to a heavily guarded room where the director of the Science Division, Nina Sharp was waiting.

"Peter, Olivia." she greeted them without preamble as they approached.

"What do we know, Nina? What have you found out about them?" Olivia asked as Nina led them into the Observation room that looked into the strangely dressed man's room.

"This one is different from the others." Nina began.

"In what ways?" Peter asked, with a cocked eyebrow as he folded his arms against his chest as he looked through the observation window at the man in question.

"He has two hearts." Nina said, pointing to the X-Rays. Peter's eyes widened at that.

"Are you sure it hasn't been double exposed or anything?"

"With our equipment? That could never happen. This man has two hearts."

"One of Bell's experiments for his ark, then?" Peter ventured.

"If these people are working for Bell, then it is highly likely." Nina nodded looking very concerned.

"Are these two awake as well?" Peter asked after a moment.

"This man appears to be in some sort of coma while the other young man is awake and restless."

"Like the red-head female I just questioned." Olivia nodded.

"Exactly." Nina nodded as she checked the strange two-hearted man's vitals for any changes.

"So, why isn't this one waking up then? Is it something to do with his additional heart?" Olivia asked, nodding her head to indicate the man in the coma through the window.

"Our best scientists have been trying to figure out, but they are stumped."

"I think it's about time we brought Walter in." Peter nodded, retrieving his phone from his jeans' back pocket.

"I couldn't agree more." Nina nodded as she left the two of them in the observation room.

Olivia continued to watch the unconscious man through the observation glass while Peter called and filled in Walter about the three mysterious people that had crashed into their lives.

"Alright, we'll see you in ten." Peter said as he ended the call.

"What does Walter think?" Olivia asked as Peter put his phone back in his pocket.

"He won't say until he can examine them for himself. He was a bit distracted by the little blue box they arrived in. He says it's a Police Public Call Box from England dating back to the early 60s at least, if not earlier. He says he can't even get inside it as the doors seem to be sealed shut."

"I can get in when we get back to the lab later." Olivia smiled at him knowingly.

"Of course you can, Liv." he nodded as they left the room to wait for Walter and Astrid to arrive.

"Hey, why don't you see if you can get anything out of the husband while we wait?" Olivia said, stopping in her tracks.

"Husband?" Peter asked, not quite following her.

"The woman and the other man both were wearing wedding rings when they were brought in..." Olivia said, always the observant one with the photographic memory.

"Ah, right." Peter nodded as he made his way to the husband's room down the hall.

Rory was beyond peeved now. He was furious. Why was he being kept prisoner on this strange planet? What had he done to deserve this? And, where exactly were his wife, Amy, and the Doctor? _Probably off on another adventure without me as usual,_ he thought bitterly as he fought against his restraints.

Suddenly a man dressed in a black suit and tie with a fedora appeared in the room. All thoughts ceased in Rory's head. How was that even possible? The room was empty save for him a moment ago and this man simply appeared out of thin air. It was almost like the TARDIS materialising...

"Who are you?" he demanded, not quite certain if he should be afraid or not of this stranger.

He was startled when the strange man seemed to speak his exact words the same moment he uttered them. It was like the stranger was a telepath or something. Rory felt goosebumps shoot down his arms and back.

"How are you doing this?" he tried, but the same thing happened once more with the man seeming to know his exact words and speaking in unison with him. It was beyond creepy.

Rory decided to close his mouth and see what the man did in response to silence. He simply stared at the man, silently challenging him to do something or say something else.

Finally after a tense moment, the stranger finally opened his mouth to speak. And, what he had to say was very ominous, indeed. "I have come to tell you something, Rory Williams."

Rory's eyes widened at that. How did this strange man know who he was? And, what exactly had he come to tell him? His thoughts and the stranger's message was interrupted when the door opened and a young man entered.

"September! What are you doing here?" the young man demanded.

"I must go now." the stranger said before abruptly vanishing once more.

"What did he say to you?" the young man demanded as he turned to Rory.

"Who was that? Where did he go?" Rory demanded at the same time.

The two men stared at each other for a tense moment. Rory decided to remain silent and not to answer any of the man's questions until he got answers.

"What did he say to you?" the young man repeated once more, growing increasingly demanding.

Rory kept his mouth shut and glared at him.

"The silent treatment? We can still get information out of you without you speaking." the young man smirked before exiting the room, leaving Rory alone once again.

Rory sighed. What was going on?

Peter angrily slammed the door shut before locking it. Olivia placed her hand on his arm in concern as he turned to face her.

"Peter, what happened? I heard you yelling." she said softly, cupping his face in her hands.

"September was in there with him."

"What? What did he say?"

"I don't know. He vanished before I could get a word out of him."

"Well, what did the husband have to say for himself."

"Nothing beyond inquiring who September was and where he went. After that, he clammed up refusing to speak to me. He knows he has leverage now. He is fully aware he has information we want desperately."

"We'll get them to talk, Peter. Walter will think of something. And, September will be back at some point, I hope."

"I don't think he finished his message to the husband. I think I interrupted him." Peter nodded as he and Olivia sat down on a bench in the hall.

"You think he'll try to come back to him and finish his warning?"

"If I know him, he will."

"Then we''ll post guards in and outside the room at all times and check the security tapes until we catch him and find out what he has to say to this stranger."

"Good. Maybe that will help in uncovering the identities of these three." Peter nodded as the door at the end of the corridor swung open and Walter shuffled in with Astrid at his side lugging two very heavy suitcases.

"Walter, Astrid!" Olivia smiled as she walked over to meet them in the middle of the hall.

"No, I'm fine. You don't need to carry this, Olivia." Astrid smiled as Olivia offered to take one of the cases. "You have that baby to look after."

"Right." Olivia sighed. It seemed ever since she discovered she was pregnant a few weeks back, everyone was being very careful around her and treating her like an invalid. She hated it.

"So, how are we going to question them? I know we've questioned recently deceased individuals in the past but we've never interrogated a live person with those methods, have we?" Astrid inquired looking at Olivia and Peter.

That, Peter knew, was the question of the hour. How, exactly, did they plan on getting any information out of the subjects when they were all alive. Corpses he felt confident that they could get answers out of, but living, breathing bodies was a whole different matter entirely. He let out a sigh and looked at his father, Dr. Walter Bishop, to explain how they would accomplish such a feat.


End file.
